Magic RNA editing!

One of those wacky Intelligent Design creationists (Jonathan McLatchie, an arrogant ignoramus I’ve actually met in Scotland) has a theory, which is his, to get around that obnoxious problem of pseudogenes. Pseudogenes are relics, broken copies of genes that litter the genome, and when you’ve got a gang of ideologues who are morally committed to the idea that every scrap of the genome is designed and functional, they put an obvious crimp in their claims.

So here’s this shattered gene littered with stop codons and with whole exons deleted and gone; how are you gonna call that “functional”, creationist? McLatchie’s solution: declare that it must still be functional, it’s just edited back into functionality. He uses the example of GULOP, a gene responsible for vitamin C synthesis, which is pretty much wrecked in us. Nonfunctional. Missing big bits. Scrambled. With missing regulatory elements, so it isn’t even transcribed. No problem: it’s just edited.

As I mentioned previously, the GULO gene in humans is rendered inactive by multiple stop codons and indel mutations. These prevent the mRNA transcript of the gene from being translated into a functional protein. If the GULO gene really is functional in utero, therefore, presumably it would require that the gene’s mRNA transcript undergo editing so that it can produce a functional protein. It’s not at all difficult to understand how this could occur.

Yes, RNA editing is a real thing. RNA does get processed before it’s translated into protein. McLatchie has a teeny-tiny bit of knowledge and is abusing it flagrantly.

I’ve hammered out dents in a car, and I’ve touched up rust spots with a little steel wool and a can of spray paint. My father was also an auto mechanic and could do wonders with a wrench. Auto repair exists, therefore…

old-wrecked-car-outback-australia-14466708

…patching up that vehicle should be no problem at all, right? I expect to see it cruisin’ down the highway any time now.

Maybe two cans of spray paint this time…?

Just in time for my cancer class

In a few weeks, we’ll be having a discussion of the ethics of cancer research: what is a reasonable intervention in the case of a patient who has no hope of survival? And look at the interesting case that just appeared on my radar: two cancer surgeons who treated brain tumors by deliberately infecting them with bacteria.

Two UC Davis neurosurgeons who intentionally infected three brain-cancer patients with bowel bacteria have resigned their posts after the university found they had "deliberately circumvented" internal policies, "defied directives" from top leaders and sidestepped federal regulations, according to newly released university documents.

Dr. J. Paul Muizelaar, 66, the former head of the neurosurgery department, and his colleague, Dr. Rudolph J. Schrot, violated the university’s faculty code of conduct with their experimental work, one internal investigation concluded.

All three patients consented to the procedures in 2010 and 2011. Two of the patients died within weeks of their surgeries, while the other survived more than a year after being infected.

The premise behind their experimental procedure is probiotics, which immediately throws a warning on the play: there’s a lot of abuse of the concept out there.

Muizelaar and Schrot called their novel approach “probiotic intracranial therapy,” or the introduction of live bowel bacteria, Enterobacter aerogenes, directly into their patients’ brains or bone flaps. The doctors theorized that an infection might stimulate the patients’ immune systems and prolong their lives.

But there are some serious problems here. They didn’t have institutional review and approval of their procedure! That’s not a warning flag, it immediately calls the entire research into question and brings the ethics of the doctors under the microscope. You don’t get to do that.

And then there’s their logic. This is a disease with a median survival of 15 months. Their first patient died less than 6 weeks after the surgery, while the second lived for a year, which the report says “buoyed the doctors and seemed to bolster their theory”. That makes no sense at all — with so few trials they can’t possibly make that kind of assessment. Furthermore, their third patient died of sepsis.

At least it sounds like we’ll have something to talk about. That seems a paltry reward for three people’s deaths.

(via The Tree of Life)

Now I feel…filthy

Earlier this week, I argued that some people didn’t understand creation-speak — they were interpreting a Ken Ham statement as an admission that he had no evidence. This was not correct, because Ken Ham is so dishonest or deluded that he’d never admit that, ever.

Now Ham has acknowledged my ‘assistance’.

Interestingly, even one of our most vocal opponents—who is an atheist—pointed out the misrepresentations made about this radio program. Dr. PZ Myers of Minnesota, who does not like me at all and hates God, has recognized that many of his fellow secularists have misquoted me and have taken my comments out of context. He wrote on his blog a few days ago that secular bloggers have completely misread my radio statements: “What he [i.e., me] actually said is familiar creationist dogma, and comes nowhere near their interpretation. . . . It doesn’t say what they think it says. Notice the ‘solely’; creationists will claim that they are using their reason, even when they aren’t.” Later in his blog, Myers takes a shot at me, but in this rare instance, PZ’s blog has come to my defense! (I am reluctant to link to PZ’s blog because of some vile content and profanity, but some people will want to check out the “defense” for themselves at freethoughtblogs.com/pharyngula.)

Yuck. I need a shower. That’s also the most he’s ever acknowledged my existence.

By the way, I don’t hate gods — they don’t exist. I really despise the buffoons who lie about gods to fleece their flocks, though.

It’s good to be annoying the Christians again

So I wrote this short essay for the Washington Post, and it’s been interesting reaching a whole different audience. It’s not an audience that is increasing my esteem for the human race, unfortunately, but it’s been…different. My twitter stream has been flooded by irate Christians, which is fun, but most of their responses are rather familiar.

Here’s one common flavor: patronizing Christian sympathy.

Berth2020 @berth2020
@washingtonpost @pzmyers you need to work on being kind to others. . I’m sorry you’ve been hurt.

I haven’t been hurt, and I don’t consider wallowing in lies as you do to be “kind”.

Then there’s the usual stereotyping of atheists as amoral monsters.

romesh sharma1949 @romesh1949
@washingtonpost @pzmyers Atheist,a man who is answerable to None, free from all bonds , will behave like an animal 99.99% or saint 00.01%

Right, Mr Made-Up-Statistics. So the prisons must be like 99.99% atheist?

Then, of course, there are the excuses.

Christopher Dull @PaEvengelist
@jeremydavidpare @DavisRBr @washingtonpost @pzmyers One reason for unanswered prayer is God does not here the prayers of unrepentant sinners

Interesting. So if you pray, and you don’t get what you want, you must be one of those unrepentant sinners? What are the other reasons?

But the most common complaint, the one that seems to be winning the votes right now, surprises me a bit.

Jeremy @jeremydavidpare
@pzmyers almost nothing you said in that article even remotely resembles anything Christian’s believe or practice… #misinformedatheist

This particular guy sent out a dozen tweets calling for his buddies to refute me; another fellow repeatedly demanded that the Washington Post allow him equal time to rebut my inaccuracies. I haven’t told the truth about Christianity!

What? Let me remind you of what my essay was about: I talked about the baggage we atheists have freed ourselves from, and I gave very general examples, stuff that is widely true of most of the diverse Christian sects in this country. Here’s a shorter version of what I mentioned.

1. No church and no sermons.

The practice of Christianity in this country certainly does involve church attendance, and it’s customary in most faiths (with exceptions, like the Quakers) to have a priest lecture you on proper behavior and beliefs at these events.

2. No heaven or hell, no bribes or threats.

Again, most Christian sects have notions of reward and punishment in an afterlife.

3. No prayers.

Every version of Christianity I’ve experienced is prayer-soaked — a combination of entreaties and worship of an invisible deity. How can anyone deny this?

4. No guilt about defying a deity.

A common Christian command is to OBEY god, one and only one god. You will be punished if you disobey. Of course there’s a burden of guilt for failure to do as the priest tells you to do!

5. No power from above, no hierarchies.

With rare exceptions (again, Quakers), most Christian sects lay out a very specific hierarchy of power and responsibilities — with Catholicism the most obvious, with power from God to Pope to Cardinals to Bishops to Priests to the laity.

6. No false consolation at death.

Another really common feature of Christianity: just go to a funeral. Look at the political cartoons after a famous person dies. “They’re in a better place,” everyone says. Wrong, say I, they’re dead and lost to us forever, and mourning is the right and proper response.

Nothing I said was in the slightest bit inaccurate; these are general properties of the practice of religion in this country. So what could they possibly argue that I was wrong about?

I have a guess. They’re going to deliver some pious hokum about the True Meaning of Faith™, which will be some pablum about redemption by the torture/execution of a fanatical Jewish preacher in the first century CE, and how the important part of Christianity is love and fellowship and spreading the gospel of our Lord, Jesus Christ, and the story of our immortal, eternal god who died and bounced back a day and a half later, since he was able to perform a Resurrection spell (but unfortunately, was unable to Cure Light Wounds so he had to walk around with holes in his hands).

Which means I forgot to include an important piece of baggage we atheists don’t have to haul around.

7. We don’t have to pretend to believe in obvious bullshit.

I’ve never been to San Diego’s Creationist “Museum”

But at least now I have a photo tour. It’s predictable, and says pretty much the same stuff as the one in Kentucky, or the one in Missouri, or the one in Washington state…they really don’t have any evidence or any story that’s worth sharing in a great big building.

Go read the first page of the Bible. You’ll have the total shebang right there, including the totality of what they’re calling evidence.

Although I do think this one photo is a nice summary of the entirety of bogus creationist logic.

thatsit

Sanal Edamaruku writes about his friend, Narendra Dabholkar

It’s sad reading. Dabholkar was clearly a good man.

Dabholkar was hated by fundamentalists. But, being the peaceful, open-hearted and kind man he was, he was adored and loved by the people. Over the years, his popularity in Maharashtra grew and grew – together with public understanding of the importance of the rationalist fight.

Stories like this make me wonder. We can praise the dead and we can talk about the good he had done, but we don’t hear the conversations of the cowards who shot him in the back, and their defenders. I’d like to see what they have to say, because I’m confident that their words would be even more persuasive of the rightness of Dabholkar’s cause.